It's not without some irony that now, a program started by a Republican governor is being undermined by a Democratic one, with bipartisan help from the Legislature.

In the latest state budget, Gov. Andrew Cuomo and lawmakers agreed to a $41 million raid of the funds the state nets from RGGI. While it's not a direct attack on the program, it is sure to harm it nonetheless, leaving RGGI vulnerable to criticism that, in the end, it's just another tax levied on utilities and consumers under the guise of fighting climate change.

RGGI's money-raising features remain intact. The program each year auctions off emission allowances, which will decrease over time in order to lower regional CO2 emissions and encourage plants to pollute less or close. The 2014 regional cap of 91 million tons is less than half the 188-million ton cap in 2009, and will decline by 2.5 percent annually through 2020. As of September, the program had raised $1.8 billion since its inception.

But where the money goes is another matter.

RGGI was mainly supposed to fund investments in energy efficiency and renewable energy, not just plug budgets. But New York's raid threatens to change that, because the state now is using the RGGI money to pay for programs already in the budget.

True, the state can say that at least $23 million of the $41 million will go to programs related to clean energy and alternative energy tax credits. But those programs have been funded without RGGI. The rest is going to the Environmental Protection Fund — some of which is focused on energy-related programs — to make up for shortfalls there.

The problem with this is that it diminishes the state's overall commitment to clean and alternative energy when that commitment should be growing. That's what RGGI was for. More dangerously, the raid will no doubt make it easier for governors and legislators to divert RGGI funds to even less relevant uses — maybe to shore up the Department of Environmental Conservation's depleted budget. In time, RGGI could easily become just another source of general fund revenue along with income taxes and fees.

We've seen this happen before with so-called dedicated funds. The lottery and gambling haven't added to education aid, but replaced tax dollars. A special fund to keep up roads and bridges is mostly just another revenue source for the Department of Transportation. And last year, Mr. Cuomo sought to use more than $500 million in clean water funds to help build a new Tappan Zee bridge, a misuse that the federal government largely nixed.

RGGI has been a solid example of how a cap-and-trade program can serve to both rein in greenhouse gas emissions and increase investment in a cleaner energy future. But it will be hard to sell to a skeptical Congress if New York turns this smart program into a shell game.